GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gloA in Pseudomonas stutzeri RCH2

Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate GFF3062 Psest_3120 lactoylglutathione lyase

Query= BRENDA::Q9HY85
         (128 letters)



>lcl|FitnessBrowser__psRCH2:GFF3062 Psest_3120 lactoylglutathione
           lyase
          Length = 130

 Score =  204 bits (518), Expect = 5e-58
 Identities = 89/124 (71%), Positives = 112/124 (90%)

Query: 1   MRILHTMIRVGNIDRSIDFYTRVLGMTLLRKNDYPDGQFTLAFVGYGNEADSAVIELTHN 60
           MR+LHTM+RVG++D+SI FYT VLGMTLLR+ DYPDG+FTLAFVGYG+EA ++VIELTHN
Sbjct: 1   MRLLHTMLRVGDMDKSIAFYTEVLGMTLLRRKDYPDGKFTLAFVGYGDEAHNSVIELTHN 60

Query: 61  WGVDAYEIGTGYGHIAIEVDDAYQACDDIRYNGGQVTREAGPMKHGTTVIAFVTDPDGYK 120
           WGV+ YE+G GYGHIA+EV+D Y+AC+DIR  GG++TRE GPM HG++++AFV DPDGYK
Sbjct: 61  WGVETYELGNGYGHIALEVEDVYKACEDIRARGGKITREPGPMMHGSSILAFVEDPDGYK 120

Query: 121 IELI 124
           IEL+
Sbjct: 121 IELL 124


Lambda     K      H
   0.321    0.140    0.421 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 130
Number of extensions: 1
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 128
Length of database: 130
Length adjustment: 14
Effective length of query: 114
Effective length of database: 116
Effective search space:    13224
Effective search space used:    13224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 41 (20.4 bits)

Align candidate GFF3062 Psest_3120 (lactoylglutathione lyase)
to HMM TIGR00068 (gloA: lactoylglutathione lyase (EC 4.4.1.5))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00068.hmm
# target sequence database:        /tmp/gapView.17056.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00068  [M=150]
Accession:   TIGR00068
Description: glyox_I: lactoylglutathione lyase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    3.5e-69  217.1   0.0    3.8e-69  217.0   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3062  Psest_3120 lactoylglutathione ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3062  Psest_3120 lactoylglutathione lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.0   0.0   3.8e-69   3.8e-69      17     143 ..       2     128 ..       1     130 [] 0.98

  Alignments for each domain:
  == domain 1  score: 217.0 bits;  conditional E-value: 3.8e-69
                           TIGR00068  17 lllhtmlrvgdldksldfytevlGmkllrkkdfpeekfslaflgyedessaavieLtynwgtekydlGngfGhia 91 
                                         +llhtmlrvgd+dks+ fytevlGm+llr+kd+p+ kf+laf+gy+de++++vieLt+nwg+e+y+lGng+Ghia
  lcl|FitnessBrowser__psRCH2:GFF3062   2 RLLHTMLRVGDMDKSIAFYTEVLGMTLLRRKDYPDGKFTLAFVGYGDEAHNSVIELTHNWGVETYELGNGYGHIA 76 
                                         79************************************************************************* PP

                           TIGR00068  92 iavddvykacervkakGgkvvrepgpvkggtkviafvkDPDGykiellekkk 143
                                         ++v+dvykace ++a+Ggk++repgp+ +g++ +afv+DPDGykiell  k+
  lcl|FitnessBrowser__psRCH2:GFF3062  77 LEVEDVYKACEDIRARGGKITREPGPMMHGSSILAFVEDPDGYKIELLSPKR 128
                                         ************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (150 nodes)
Target sequences:                          1  (130 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 4.47
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory